28 results on '"Harpke, Dörte"'
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2. Cytogeography of Gagea bohemica (Liliaceae) outside the Mediterranean: two ploidy levels, spatial differentiation of cytotypes, and occurrence of mixed-ploidy populations
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Horák, David, Trávníček, Bohumil, Király, Gergely, Détraz-Méroz, Jacqueline, Vymyslický, Tomáš, Kozoni, Marianthi, Harpke, Dörte, and Hroneš, Michal
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- 2023
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3. Climate-driven past and present interspecies gene flow may have contributed to shape microscale adaptation capacity in Tillandsia lomas in hyperarid south American desert systems
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Stein, Ron Eric, Luque-Fernández, César R., Kiefer, Christiane, Möbus, Johanna, Pauca-Tanco, G. Anthony, Jabbusch, Sarina, Harpke, Dörte, Bechteler, Julia, Quandt, Dietmar, Villasante, Francisco, and Koch, Marcus A.
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- 2023
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4. Contrasting effects of local environment and grazing pressure on the genetic diversity and structure of Artemisia frigida
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Oyundelger, Khurelpurev, Herklotz, Veit, Harpke, Dörte, Oyuntsetseg, Batlai, Wesche, Karsten, and Ritz, Christiane M.
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- 2021
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5. Biogeography of larches in eastern Siberia – using single nucleotide polymorphisms derived by genotyping by sequencing.
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Haupt, Sarah, Bernhardt, Nadine, Killing, Stefanie, Meucci, Stefano, Herzschuh, Ulrike, Zakharov, Evgenii S., Harpke, Dörte, Pestryakova, Luidmila A., and Kruse, Stefan
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SINGLE nucleotide polymorphisms ,LAST Glacial Maximum ,BIOGEOGRAPHY ,LARCHES ,PHYLOGEOGRAPHY ,TAIGAS - Abstract
The present distribution of Siberian boreal forests that are dominated by larches (Larix spp.) is influenced, to an unknown extent, by glacial history. Knowing the past treeline dynamics can improve our understanding of future treeline shifts under changing climate. Here, we study patterns in the genetic variability of Siberian Larix to help unravel biogeographic migration routes since the Last Glacial Maximum (LGM). We infer the spatial distribution and the postglacial demographic history of Larix using genome‐wide single nucleotide polymorphisms (SNPs) derived through genotyping by sequencing (GBS) from 130 individuals sampled across eastern Siberia. Our analysis gives statistical support for two or three clusters, spanning from western to eastern Siberia. These clusters reveal a genetic structure influenced by isolation resulting from geographical distance, barriers imposed by geographic features, and distinct glacial histories. Assuming three clusters, our demographic inference indicates that the common ancestor of the current Larix populations existed in northeast Siberia well before the LGM. This suggests that Larix persisted in the northern region throughout previous glacials. Our genetic studies suggest that Larix likely survived the cold LGM in northern refugia, enabling a fast colonization of Siberia. Instead of complete repopulation from southern areas postglacially, the northernmost Larix expansion during the Holocene seems to have benefitted from refugial populations ahead of the treeline. Present‐day migration is expected to be slow initially, due to the absence of current refugial populations in the far north, in contrast to the early‐Holocene situation. [ABSTRACT FROM AUTHOR]
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- 2024
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6. Landscape genetics of the endangered Atacama Desert shrub Balsamocarpon brevifolium in the context of habitat fragmentation
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Stoll, Alexandra, Harpke, Dörte, Schütte, Claudia, Jimenez, Lissette, Letelier, Luis, Blattner, Frank R., and Quandt, Dietmar
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- 2020
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7. Morphological and molecular investigations of Gagea (Liliaceae) in southeastern Kazakhstan with special reference to putative altitudinal hybrid zones
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Peterson, Angela, Harpke, Doerte, Levichev, Igor G., Beisenova, Saltanat, Schnittler, Martin, and Peterson, Jens
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- 2016
8. Phylogeny, karyotype evolution and taxonomy of Crocus series Verni (Iridaceae)
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Harpke, Dörte, Carta, Angelino, Tomović, Gordana, Ranđelović, Vladimir, Ranđelović, Novica, Blattner, Frank R., and Peruzzi, Lorenzo
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- 2015
9. Reticulate evolution of the critical Mediterranean Gagea sect. Didymobulbos (Liliaceae) and its taxonomic implications
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Tison, Jean-Marc, Peterson, Angela, Harpke, Dörte, and Peruzzi, Lorenzo
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- 2013
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10. Hybridization drives speciation in Gagea (Liliaceae)
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Peterson, Angela, Harpke, Doerte, Peruzzi, Lorenzo, Levichev, Igor G., Tison, J.-M., and Peterson, Jens
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- 2009
11. Quantitative PCR Revealed a Minority of ITS Copies to Be Functional in Mammillaria (Cactaceae)
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Harpke, Doerte and Peterson, Angela
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- 2007
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12. Disentangling Crocus Series Verni and Its Polyploids.
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Raca, Irena, Blattner, Frank R., Waminal, Nomar Espinosa, Kerndorff, Helmut, Ranđelović, Vladimir, and Harpke, Dörte
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POLYPLOIDY ,CHLOROPLAST DNA ,GENOME size ,HETEROZYGOSITY ,GENOMICS ,CHROMOSOMES ,PLOIDY ,KARYOTYPES - Abstract
Simple Summary: In plants, the occurrence of polyploid lineages, which are plants with multiple instead of two sets of chromosomes, is quite common. Polyploids can originate as autopolyploids within a species or by combining the genomes of different species resulting in allopolyploids. Within the group of spring crocuses, a polyploid complex exists where it is unclear how it evolved and which species eventually contributed to polyploid formation. Among Crocus species, evolutionary analyses are further complicated by widely varying chromosome numbers that do not clearly correlate with di- or polyploidy. To reconstruct the evolution of these polyploids, we combine chromosome counts, genome size estimations, phylogenetic analyses based on maternally and bi-parentally inherited genomes, co-ancestry analysis, and morphometric data for all species potentially involved in polyploid formation. Through this approach, we show that polyploids in the Crocus heuffelianus group are allopolyploids that originated multiple times involving different parental genotypes and reciprocal crosses. Chromosome numbers partly changed after polyploidization. Numbers found in polyploids are therefore no longer in all cases additive values of their parents' chromosomes. We conclude that in crocuses, only an approach combining evidence from different analysis methods can uncover the evolutionary history of species if polyploidization is involved. Spring crocuses, the eleven species within Crocus series Verni (Iridaceae), consist of di- and tetraploid cytotypes. Among them is a group of polyploids from southeastern Europe with yet-unclear taxonomic affiliation. Crocuses are generally characterized by complex dysploid chromosome number changes, preventing a clear correlation between these numbers and ploidy levels. To reconstruct the evolutionary history of series Verni and particularly its polyploid lineages associated with C. heuffelianus, we used an approach combining phylogenetic analyses of two chloroplast regions, 14 nuclear single-copy genes plus rDNA spacers, genome-wide genotyping-by-sequencing (GBS) data, and morphometry with ploidy estimations through genome size measurements, analysis of genomic heterozygosity frequencies and co-ancestry, and chromosome number counts. Chromosome numbers varied widely in diploids with 2n = 8, 10, 12, 14, 16, and 28 and tetraploid species or cytotypes with 2n = 16, 18, 20, and 22 chromosomes. Crocus longiflorus, the diploid with the highest chromosome number, possesses the smallest genome (2C = 3.21 pg), while the largest diploid genomes are in a range of 2C = 7–8 pg. Tetraploid genomes have 2C values between 10.88 pg and 12.84 pg. Heterozygosity distribution correlates strongly with genome size classes and allows discernment of di- and tetraploid cytotypes. Our phylogenetic analyses showed that polyploids in the C. heuffelianus group are allotetraploids derived from multiple and partly reciprocal crosses involving different genotypes of diploid C. heuffelianus (2n = 10) and C. vernus (2n = 8). Dysploid karyotype changes after polyploidization resulted in the tetraploid cytotypes with 20 and 22 chromosomes. The multi-data approach we used here for series Verni, combining evidence from nuclear and chloroplast phylogenies, genome sizes, chromosome numbers, and genomic heterozygosity for ploidy estimations, provides a way to disentangle the evolution of plant taxa with complex karyotype changes that can be used for the analysis of other groups within Crocus and beyond. Comparing these results with morphometric analysis results in characters that can discern the different taxa currently subsumed under C. heuffelianus. [ABSTRACT FROM AUTHOR]
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- 2023
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13. Cryptic speciation shapes the biogeographic history of a northern distributed moss.
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Escolástico-Ortiz, Dennis Alejandro, Hedenäs, Lars, Quandt, Dietmar, Harpke, Dörte, Larraín, Juan, Stech, Michael, and Villarreal A, Juan Carlos
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GLACIAL Epoch ,SINGLE nucleotide polymorphisms ,MOSSES ,GENETIC variation ,ENVIRONMENTAL history ,SPECIES distribution - Abstract
Increasing evidence indicates that wide distributed bryophyte taxa with homogeneous morphology may represent separate evolutionary lineages. The evolutionary histories of these cryptic lineages may be related to historical factors, such as the climatic oscillations in the Quaternary. Thus, the post-glacial demographic signatures paired with cryptic speciation may result in complex phylogeographic patterns. This research has two aims: to determine whether the widespread moss Racomitrium lanuginosum represents cryptic molecular taxa across the Northern Hemisphere and to infer the effects of Quaternary glaciations on spatial genetic diversity. We used the internal transcribed spacer (ITS) marker to resolve the phylogeographic history of the species and single nucleotide polymorphisms (genotyping-by-sequencing) to infer the genetic structure and demographic history. Finally, we assessed the historical changes in the distribution range using species distribution models. Racomitrium lanuginosum comprises distinct molecular lineages sympatrically distributed in the Northern Hemisphere. We also uncovered long-distance dispersal from eastern North America to Scandinavia and potential in situ survival in northern Scandinavia. Due to the genetic signatures, the Alaska Peninsula could be considered a glacial refugium. The species experienced post-glacial expansion northwards in the Northern Hemisphere, mainly from the Alaska Peninsula. Our results exemplify the complex phylogeographic history in cold environments and contribute to recognizing evolutionary patterns in the Northern Hemisphere. [ABSTRACT FROM AUTHOR]
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- 2023
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14. Plant migration under long‐lasting hyperaridity – phylogenomics unravels recent biogeographic history in one of the oldest deserts on Earth.
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Böhnert, Tim, Luebert, Federico, Merklinger, Felix F., Harpke, Dörte, Stoll, Alexandra, Schneider, Julio V., Blattner, Frank R., Quandt, Dietmar, and Weigend, Maximilian
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DESERTS ,CLADISTIC analysis ,ENVIRONMENTAL history ,NUCLEOTIDE sequencing ,PLANT communities ,INTROGRESSION (Genetics) ,MOLECULAR clock - Abstract
Summary: The post‐Miocene climatic histories of arid environments have been identified as key drivers of dispersal and diversification. Here, we investigate how climatic history correlates with the historical biogeography of the Atacama Desert genus Cristaria (Malvaceae).We analyze phylogenetic relationships and historical biogeography by using next‐generation sequencing (NGS), molecular clock dating, Dispersal Extinction Cladogenesis and Bayesian sampling approaches. We employ a novel way to identify biogeographically meaningful regions as well as a rarely utilized program permitting the use of dozens of ancestral areas.Partial incongruence between the established taxonomy and our phylogenetic data argue for a complex historical biogeography with repeated introgression and incomplete lineage sorting. Cristaria originated in the central southern part of the Atacama Desert, from there the genus colonized other areas from the late Miocene onwards. The more recently diverged lineages appear to have colonized different habitats in the Atacama Desert during pluvial phases of the Pliocene and early Pleistocene.We show that NGS combined with near‐comprehensive sampling can provide an unprecedented degree of phylogenetic resolution and help to correlate the historical biogeography of plant communities with cycles of arid and pluvial phases. [ABSTRACT FROM AUTHOR]
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- 2022
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15. Ancient Artworks and Crocus Genetics Both Support Saffron's Origin in Early Greece.
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Kazemi-Shahandashti, Seyyedeh-Sanam, Mann, Ludwig, El-nagish, Abdullah, Harpke, Dörte, Nemati, Zahra, Usadel, Björn, and Heitkam, Tony
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SAFFRON crocus ,ANCIENT art ,SAFFRON (Spice) ,GENETICS ,NUCLEOTIDE sequencing - Abstract
Saffron crocus (Crocus sativus) is a male-sterile, triploid flower crop, and source of the spice and colorant saffron. For over three millennia, it was cultivated across the Mediterranean, including ancient Greece, Persia, and other cultures, later spreading all over the world. Despite saffron crocus' early omnipresence, its origin has been the matter of a century-old debate, in terms of area and time as well as parental species contribution. While remnants of the ancient arts, crafts, and texts still provide hints on its origin, modern genetics has the potential to efficiently follow these leads, thus shedding light on new possible lines of descent. In this review, we follow ancient arts and recent genetics to trace the evolutionary origin of saffron crocus. We focus on the place and time of saffron domestication and cultivation, and address its presumed autopolyploid origin involving cytotypes of wild Crocus cartwrightianus. Both ancient arts from Greece, Iran, and Mesopotamia as well as recent cytogenetic and comparative next-generation sequencing approaches point to saffron's emergence and domestication in ancient Greece, showing how both disciplines converge in tracing its origin. [ABSTRACT FROM AUTHOR]
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- 2022
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16. A new species of Crocus ser. Verni (Iridaceae) with 2n = 12 chromosomes from the Balkans.
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Raca, Irena, Harpke, Dörte, Shuka, Lulëzim, and Ranđelović, Vladimir
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SINGLE nucleotide polymorphisms , *CHROMOSOMES , *IRIDACEAE , *LEAF anatomy , *SPECIES - Abstract
A Crocus population in the Northern Albanian Alps obviously belonging to C. ser. Verni was referred to C. heuffelianus, but closer field investigations revealed that it could not be identified with this or any other Verni species. The detailed description of a new species, Crocus bertiscensis, including morphology, leaf anatomy, cytology, and phylogenetic relationship is provided and illustrated. Phylogenetic analyses based on genome-wide single nucleotide polymorphism data obtained through genotyping-by-sequencing placed C. bertiscensis as clearly distinct from C. heuffelianus, supporting its rank as a species within C. ser. Verni. Morphologically, it differs from C. heuffelianus by showing paler and flatter perigone segments, short perigone tubes and leaf white stripe width of 1/7 compared to the leaf diameter. Finally, karyological and molecular analysis revealed that C. bertiscensis applies to the 2n = 12 cytotype of C. heuffelianus from Čakor Pass area reported by earlier studies. [ABSTRACT FROM AUTHOR]
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- 2022
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17. Phylogeography of Artemisia frigida (Anthemideae, Asteraceae) based on genotyping‐by‐sequencing and plastid DNA data: Migration through Beringia.
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Oyundelger, Khurelpurev, Harpke, Dörte, Herklotz, Veit, Troeva, Elena, Zheng, Zhenzhen, Li, Zheng, Oyuntsetseg, Batlai, Wagner, Viktoria, Wesche, Karsten, and Ritz, Christiane M.
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PHYLOGEOGRAPHY , *GRASSLANDS , *ARTEMISIA , *SPECIES distribution , *ASTERACEAE - Abstract
Artemisia frigida is a temperate grassland species that has the largest natural range among its genus, with occurrences across the temperate grassland biomes of Eurasia and North America. Despite its wide geographic range, we know little about the species' distribution history. Hence, we conducted a phylogeographical study to test the hypothesis that the species' distribution pattern is related to a potential historical migration over the 'Bering land bridge'. We applied two molecular approaches: genotyping‐by‐sequencing (GBS) and Sanger sequencing of the plastid intergenic spacer region (rpl32 – trnL) to investigate genetic differentiation and relatedness among 21 populations from North America, Middle Asia, Central Asia and the Russian Far East. Furthermore, we identified the ploidy level of individuals based on GBS data. Our results indicate that A. frigida originated in Asia, spread northwards to the Far East and then to North America across the Bering Strait. We found a pronounced genetic structuring between Middle and Central Asian populations with mixed ploidy levels, tetraploids in the Far East, and nearly exclusively diploids in North America except for one individual. According to phylogenetic analysis, two populations of Kazakhstan (KZ2 and KZ3) represent the most likely ancestral diploids that constitute the basally branching lineages, and subsequent polyploidization has occurred on several occasions independently. Mantel tests revealed weak correlations between genetic distance and geographical distance and climatic conditions, which indicates that paleoclimatic fluctuations may have more profoundly influenced A. frigida's spatial genetic structure and distribution than the current environment. [ABSTRACT FROM AUTHOR]
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- 2022
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18. Saffron (Crocus sativus) is an autotriploid that evolved in Attica (Greece) from wild Crocus cartwrightianus.
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Nemati, Zahra, Harpke, Dörte, Gemicioglu, Almila, Kerndorff, Helmut, and Blattner, Frank R.
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SAFFRON crocus , *CHLOROPLAST DNA , *GENOME size , *VEGETATIVE propagation , *RADISHES - Abstract
• GBS data infer an autotriploid origin of saffron derived from Crocus cartwrightianus. • Saffron evolved and was domesticated in Attica (Greece). • New saffron types might be synthesized from different C. cartwrightianus genotypes. Crocus sativus , the saffron crocus, is the source of saffron, which is made from the dried stigmas of the plant. It is a male-sterile triploid lineage that ever since its origin has been propagated vegetatively. Its mode of evolution and area of origin are matters of long-lasting debates. Here we analyzed chloroplast genomes and genome-wide DNA polymorphisms obtained through genotyping-by-sequencing (GBS) to infer the parent and area of origin of C. sativus. These data were complemented by genome size measurements and analyses of nuclear single-copy genes. We could place 99.3% of saffron GBS alleles in Crocus cartwrightianus , a species occurring in southeastern mainland Greece and on Aegean islands, identifying it as the sole progenitor of the saffron crocus. Phylogenetic and population assignment analyses together with chloroplast polymorphisms indicated the C. cartwrightianus population in the vicinity of Athens as most similar to C. sativus. We conclude that the crop is an autotriploid that evolved in Attica by combining two different genotypes of C. cartwrightianus. Triploid sterility and vegetative propagation prevented afterwards segregation of the favorable traits of saffron, resulting in worldwide cultivation of a unique clonal lineage. [ABSTRACT FROM AUTHOR]
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- 2019
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19. A pre‐Miocene Irano‐Turanian cradle: Origin and diversification of the species‐rich monocot genus Gagea (Liliaceae).
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Peterson, Angela, Harpke, Dörte, Peterson, Jens, Harpke, Alexander, and Peruzzi, Lorenzo
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RIBOSOMAL DNA , *LILIACEAE , *MOLECULAR clock , *SPECIES distribution , *NUCLEOTIDE sequence - Abstract
The Irano‐Turanian (IT) floristic region is considered an important center of origin for many taxa. However, there is a lack of studies dealing with typical IT genera that also occur in neighboring areas. The species‐rich monocot genus Gagea Salisb. shows a center of diversity in IT region and a distribution in adjacent regions, therefore representing a good study object to investigate spatial and temporal relationships among IT region and its neighboring areas (East Asia, Euro‐Siberia, Himalaya, and Mediterranean). We aimed at (a) testing the origin of the genus and of its major lineages in the IT region, (b) reconstructing divergence times, and (c) reconstructing colonization events. To address these problems, sequences of the ribosomal DNA internal transcribed spacer (ITS) region of 418 individuals and chloroplast intergenic spacers sequences (psbA‐trnH, trnL‐trnF) of 497 individuals, representing 116 species from all sections of the genus and nearly its entire distribution area were analyzed. Divergence times were estimated under a random molecular clock based on nrITS phylogeny, which was the most complete data set regarding the representation of species and distribution areas. Ancestral distribution ranges were estimated for the nrITS data set as well as for a combined data set, revealing that Gagea most likely originated in southwestern Asia. This genus first diversified there starting in the Early Miocene. In the Middle Miocene, Gagea migrated to the Mediterranean and to East Asia, while migration into Euro‐Siberia took place in the Late Miocene. During the Pleistocene, the Arctic was colonized and Gagea serotina, the most widespread species, reached North America. The Mediterranean basin was colonized multiple times from southwestern Asia or Euro‐Siberia. Most of the currently existing species originated during the last 3 Ma. [ABSTRACT FROM AUTHOR]
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- 2019
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20. Development of microsatellite markers and assembly of the plastid genome in Cistanthe longiscapa (Montiaceae) based on low-coverage whole genome sequencing.
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Stoll, Alexandra, Harpke, Dörte, Schütte, Claudia, Stefanczyk, Nadine, Brandt, Ronny, Blattner, Frank R., and Quandt, Dietmar
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MICROSATELLITE repeats , *PLASTIDS , *GENOMES , *POLYMERASE chain reaction , *PHYLOGEOGRAPHY - Abstract
Cistanthe longiscapa is an endemic annual herb and characteristic element of the Chilean Atacama Desert. Principal threats are the destruction of its seed deposits by human activities and reduced germination rates due to the decreasing occurrence of precipitation events. To enable population genetic and phylogeographic analyses in this species we performed paired-end shotgun sequencing (2x100 bp) of genomic DNA on the Illumina HiSeq platform and identified microsatellite (SSR) loci in the resulting sequences. From 29 million quality-filtered read pairs we obtained 549,174 contigs (average length 614 bp; N50 = 904). Searching for SSRs revealed 10,336 loci with microsatellite motifs. Initially, we designed primers for 96 loci, which were tested for PCR amplification on three C. longiscapa individuals. Successfully amplifying loci were further tested on eight individuals to screen for length variation in the resulting amplicons, and the alleles were exemplarily sequenced to infer the basis for the observed length variation. Finally we arrived at 26 validated SSR loci for population studies in C. longiscapa, which resulted in 146 bi-allelic SSR markers in our test sample of eight individuals. The genomic sequences were also used to assemble the plastid genome of C. longiscapa, which provides an additional set of maternally inherited genetic markers. [ABSTRACT FROM AUTHOR]
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- 2017
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21. Phylogeny, geographic distribution, and new taxonomic circumscription of the Crocus reticulatus species group (Iridaceae).
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HARPKE, Dörte, PERUZZI, Lorenzo, KERNDORFF, Helmut, KARAMPLIANIS, Theophanis, CONSTANTINIDIS, Theophanis, RANÐELOVIC, Vladimir, RANÐELOVIC, Novica, JUŠKOVIC, Marina, PASCHE, Erich, and BLATTNER, Frank R.
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PHYLOGENY , *BIOLOGICAL classification , *CROCUSES , *PLANT species , *IRIDACEAE , *DATA analysis - Abstract
Recent phylogenetic analyses proved several infrageneric units within the genus Crocus to be para- or polyphyletic. In an attempt to arrive at a system of Crocus that closely reflects species relationships, we provide here phylogenetic, morphometric, geographic, and nomenclatorial data for the species of a narrower-defined, monophyletic Crocus series Reticulati. We sequenced the ETS and ITS regions of the nuclear ribosomal DNA in 9 Reticulati and 19 outgroup species. Three chloroplast loci (trnL-F, rps16-trnQ, matK-trnK) were sequenced in the newly defined series Reticulati species and 1 outgroup. Data were analyzed with Bayesian and parsimony algorithms. The phylogenies resulted in 2 clearly separated, geographically defined species groups within the series Reticulati. The southern one comprises only the taxa from Turkey, while the species of the second group are distributed from Italy in the west through the areas north of the Black Sea to the Caucasus in the east. To arrive at monophyletic species we describe here C. danubensis sp. nov., C. filis-maculatis sp. nov., and C. orphei sp. nov. as new species, and we define C. reticulatus s.s. to comprise only the populations in the area north and east of the Black Sea. [ABSTRACT FROM AUTHOR]
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- 2014
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22. Phylogeny of Crocus (Iridaceae) based on one chloroplast and two nuclear loci: Ancient hybridization and chromosome number evolution
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Harpke, Dörte, Meng, Shuchun, Rutten, Twan, Kerndorff, Helmut, and Blattner, Frank R.
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PHYLOGENY , *CROCUSES , *CHLOROPLASTS , *LOCUS (Genetics) , *SPECIES hybridization , *PLOIDY - Abstract
Abstract: Crocus consists of about 100 species distributed from western Europe and northern Africa to western China, with the center of diversity on the Balkan Peninsula and in Asia Minor. Our study focuses on clarifying phylogenetic relationships and chromosome number evolution within the genus using sequences of the chloroplast trnL-F region, the nuclear ribosomal DNA internal transcribed spacer (ITS) region, and a part of the nuclear single-copy gene pCOSAt103. In a combined dataset of ITS and trnL-F sequences, 115 individuals representing 110 taxa from both subgenera and all sections and series of Crocus were analyzed with Bayesian phylogenetic inference. For pCOSAt103 79 individuals representing 74 Crocus taxa were included, and for the majority of them PCR amplicons were cloned and up to eight clones per individual were sequenced to detect allopolyploidization events. Romulea species were included as outgroup in both analyses. Characteristics of seed surface structures were evaluated by scanning electron microscopy. Phylogenetic analysis of ITS/trnL-F data resulted in a monophyletic genus Crocus, probably monophyletic sections Crocus and Nudiscapus, and inferred monophyly for eight of the 15 series of the genus. The C. biflorus aggregate, thought to be consisting of closely related subspecies, was found to be polyphyletic, the taxa occurring within three major clades in the phylogenetic tree. Cloning of pCOSAt103 resulted in the detection of homoeologous copies in about one third of the taxa of section Nudiscapus, indicating an allotetraploid origin of this section. Reconstruction of chromosome number evolution along the phylogenetic tree using a probabilistic and a parsimony approach arrived at partly contradictory results. Both analyses agreed however on the occurrence of multiple polyploidization and dysploidy events. B chromosomes evolved at least five times independently within the genus, preferentially in clades characterized by karyotype changes. [Copyright &y& Elsevier]
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- 2013
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23. New light on phylogeny and taxonomy of the Eurasian Gagea villosa- G. fragifera complex (Liliaceae).
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Peruzzi, Lorenzo, Peterson, Angela, Tison, Jean-Marc, and Harpke, Dörte
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PHYLOGENY ,LILIACEAE ,TAXONOMY ,VILLOSA ,POLYPLOIDY ,SPECIES hybridization - Abstract
The typification of the name Gagea brentae Evers (a lectotype in GZU is designated here) and studies of living topotype material, led us to conclude that G. brentae is a full synonym of G. fragifera, sharing morphological, karyological (2n=84) and molecular (ITS region, trnL- trnF IGS, psbA- trnH IGS) features with the latter species. Gagea fragifera, as newly circumscribed here, shows a close relationship with G. villosa (M. Bieb.) Sweet and, above all, with G. glacialis K. Koch (possibly a hybridogenous taxon). In short, our new morphological and molecular data provide new evidence for hybridization and introgression between the closely related G. villosa and G. fragifera (both in G. sect. Didymobulbos). [ABSTRACT FROM AUTHOR]
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- 2012
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24. New microsatellite markers for Xerophyta dasylirioides (Velloziaceae), an endemic species on Malagasy inselbergs.
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Rexroth, Juliane, Krebes, Lukas, Wöhrmann, Tina, Harpke, Dörte, Rabarimanarivo, Marina, Phillipson, Peter, Weising, Kurt, and Porembski, Stefan
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MICROSATELLITE repeats ,SHOTGUN sequencing ,HETEROZYGOSITY ,GENE flow ,SPECIES ,PARAMETERS (Statistics) ,ALLELES - Abstract
Premise: Microsatellite markers were developed for Xerophyta dasylirioides (Velloziaceae), a species endemic to the Malagasy inselbergs, to explore the impact of its island‐like distribution on genetic diversity and gene flow. Methods and Results: A total of 7110 perfect microsatellite loci were recovered by shotgun sequencing on an Illumina MiSeq platform. Primer pairs were designed for 40 arbitrarily selected loci. Fifteen primer pairs that generated distinct PCR products were used to genotype 80 individuals of X. dasylirioides from three inselberg populations. All markers were polymorphic, revealing two to 17 alleles in the overall sampling. Levels of observed and expected heterozygosity per locus ranged from zero to 1.000 and from zero to 0.850, respectively. Success rates of cross‐amplification in 10 additional species of Xerophyta (X. croatii, X. decaryi, X. isaloensis, X. labatii, X. lewisiae, X. pinifolia, X. retinervis, X. setosa, X. spekei, X. tulearensis) ranged from zero to 70%. Conclusions: Fifteen newly developed microsatellite markers provide a toolkit for assessing population genetic parameters of X. dasylirioides in its unique island‐like habitats. [ABSTRACT FROM AUTHOR]
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- 2019
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25. Phylogeny of the saffron-crocus species group, Crocus series Crocus (Iridaceae).
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Nemati, Zahra, Blattner, Frank R., Kerndorff, Helmut, Erol, Osman, and Harpke, Dörte
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PHYLOGENY , *IRIDACEAE , *SAFFRON crocus , *RIBOSOMAL DNA , *CROCUSES , *SINGLE nucleotide polymorphisms - Abstract
Phylogenetic relationships among the taxa of Crocus series Crocus are still unclear, preventing the understanding of species diversity and the evolution of the important spice saffron ( Crocus sativus ). Therefore, we analyzed sequences of two chloroplast ( trn L- trn F, mat K- trn K) and three nuclear (TOPO6, ribosomal DNA ETS and ITS) marker regions to infer phylogenetic relationships among all species belonging to series Crocus . Our phylogenetic analyses resolved the relationships among all taxa of the series. Crocus hadriaticus and the former C. pallasii subspecies appeared polyphyletic. The latter deserve elevating the subspecies to species rank, while for C. hadriaticus a detailed study of species boundaries is necessary. Multi-locus and also genome-wide single nucleotide polymorphism data obtained through genotyping-by-sequencing placed C. sativus within C. cartwrightianus with no indication that other Crocus species contributed to the evolution of the triploid. Our analyses thus made an autotriploid origin of C. sativus from C. cartwrightianus very likely. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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26. Range expansion and contraction of Tillandsia landbeckii lomas in the hyperarid Chilean Atacama Desert indicates ancient introgression and geneflow.
- Author
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Koch, Marcus A., Kiefer, Christiane, Möbus, Johanna, Quandt, Dietmar, Merklinger, Felix, Harpke, Dörte, and Benavides, Francisco Villasante
- Subjects
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BROMELIACEAE , *COLONIZATION (Ecology) , *GENOMICS , *DESERTS , *DESERT plants , *VASCULAR plants - Abstract
Among the fascinating and highly specialized vascular plants in the hyperarid core of the Chilean and Peruvian Atacama Desert there are few Tillandsia species from the bromeliad family (Bromeliaceae). These grow epiarenically on bare sand without a functional root system, and in some rare cases they build up a monospecific and often the only landscape characterizing vegetation type, which is called Tillandsiales or Tillandsia loma. Tillandsia landbeckii is the dominating epiarenic species in Chile totally dependent on fog serving as the only water resource. Herein we elaborate on the hypothesis that migration and multiple colonization in concert with putative introgression from other Tillandsia species build up the present day phylogeographic distribution pattern and may contribute to the evolutionary dynamics and long-term success in hyperarid desert systems. Genomic analyses using GBS (genotyping-by-sequencing) data from the nuclear and plastid genome were conducted at the population level. A genome skimming approach was used to generate reference plastome data. The results indicate that both, multiple colonization and secondary contact of old gene pools and interspecies geneflow, contribute to present-day population genetic structure. Local-scale analysis also indicates that these past footprints of evolutionary history do contribute to present-day local adaptive potential of the species. • Evolutionary history of hyperarid Atacama Desert plants. • Intra- and interspecies geneflow shape genetic architecture of gene pools. • Population structure reflects ancient migration. [ABSTRACT FROM AUTHOR]
- Published
- 2022
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27. Resolving relationships in an exceedingly young Neotropical orchid lineage using Genotyping-by-sequencing data.
- Author
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Pérez-Escobar, Oscar Alejandro, Bogarín, Diego, Schley, Rowan, Bateman, Richard M., Gerlach, Günter, Harpke, Dörte, Brassac, Jonathan, Fernández-Mazuecos, Mario, Dodsworth, Steven, Hagsater, Eric, Blanco, Mario A., Gottschling, Marc, and Blattner, Frank R.
- Subjects
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ORCHIDS , *PHENOMENOLOGICAL biology , *SPECIES hybridization , *PHYLOGENY , *SUBSPECIES - Abstract
• Genotyping-by-sequencing (GBS) is widely employed in phylogenomics. • We employ GBS to resolve relationships within a recalcitrant orchid species complex. • About 50% of GBS loci recovered lack phylogenetic informativeness (PI) • The PI of the 42 most informative GBS loci is comparable with that of nrITS. • Phylogenomics of GBS datasets recircumscribes six prior taxa as only three species. Poor morphological and molecular differentiation in recently diversified lineages is a widespread phenomenon in plants. Phylogenetic relationships within such species complexes are often difficult to resolve because of the low variability in traditional molecular loci. Furthermore, biological phenomena responsible for topological incongruence such as Incomplete Lineage Sorting (ILS) and hybridisation complicate the resolution of phylogenetic relationships among closely related taxa. In this study, we employ a Genotyping-by-sequencing (GBS) approach to disentangle evolutionary relationships within a species complex belonging to the Neotropical orchid genus Cycnoches. This complex includes seven taxa distributed through Central America and the Colombian Chocó, and is nested within a clade estimated to have first diversified in the early Quaternary. Previous phylogenies inferred from few loci failed to provide support for internal relationships within the complex. Our Neighbour-net and coalescent-based analyses inferred from ca. 13,000 GBS loci obtained from 31 individuals belonging to six of the seven traditionally accepted Cycnoches taxa provided a robust phylogeny for this group. The genus Cycnoches includes three main clades that are further supported by morphological traits and geographic distributions. Similarly, a topology reconstructed through maximum likelihood (ML) inference of concatenated GBS loci produced results that are comparable with those reconstructed through coalescence and network-based methods. Our comparative phylogenetic informativeness analyses suggest that the low support evident in the ML phylogeny might be attributed to the abundance of uninformative GBS loci, which can account for up to 50% of the total number of loci recovered. The phylogenomic framework provided here, as well as morphological evidence and geographical patterns, suggest that the six entities previously thought to be different species or subspecies might actually represent only three distinct segregates. We further discuss the limited phylogenetic informativeness found in our GBS approach and its utility to disentangle relationships within recent and rapidly evolving species complexes. Our study is the first to demonstrate the utility of GBS data to reconstruct relationships within young (~2 Ma) Neotropical plant clades, opening new avenues for studies of species complexes that populate the species-rich orchid family. [ABSTRACT FROM AUTHOR]
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- 2020
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28. Relationship Between Genetic and Phenotypic Variations in Natural Populations of Perennial and Biennial Sagebrush.
- Author
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Oyundelger K, Großmann L, Herklotz V, Harpke D, Batlai O, Wesche K, and Ritz CM
- Abstract
Plant responses to environmental heterogeneity depend on life-history traits, which could relate to phenotypical and genetic characteristics. To elucidate this relationship, we examined the variation in population genetics and functional traits of short- and long-lived Artemisia species that are co-occurring in the steppes of Mongolia. Mongolian steppes represent stressful and water-limited habitats, demanding phenotypic modifications in the short term and/or genetic adaptation in the long term. However, detailed knowledge is missing about both plant phenotypic and genetic differentiation, and their interrelationships in temperate grasslands. Here, we investigated 21 populations of the widely distributed subshrub Artemisia frigida and the herbaceous biennial Artemisia scoparia . Genetic variation was assessed with newly developed simple sequence repeats (SSRs) markers. Functional trait data were collected from each individual, and data on environmental variables was collected for each population. We detected significantly higher genetic diversity in the biennial species ( H
E = 0.86) compared with the perennial ( HE = 0.79). For both species, the largest share of genetic variation was partitioned within populations (96%). Population genetic structure in the biennial A. scoparia was weak, while the perennial A. frigida showed some spatial genetic structure, which was impacted by geographical factors, soil nutrients, and precipitation amount. Morphology-related functional traits (i.e., plant height) were predominantly associated with environmental variables rather than with genetic variation, whereas physiology-related trait (i.e., specific leaf area [SLA]) was partly genetically determined., Competing Interests: The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Khurelpurev Oyundelger reports financial support was provided by TU Dresden. Karsten Wesche reports travel was provided by German Federal Ministry of Education and Research. Christiane Ritz reports travel was provided by German Academic Exchange Service., (© 2024 The Author(s). Ecology and Evolution published by John Wiley & Sons Ltd.)- Published
- 2024
- Full Text
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